RNA-Seq: differential expression analysis of controls (literature)

Libraries required

library(plotly)

Data

load("input/limma_SC_Controls.RData")
lab <- dea.limma

load("input/limma_SC_Controls_lit.RData")
lit <- dea.limma

logFC comparison

PND7/8 vs PND14/15

lab.fc.pnd <- lab$`PND8 vs PND15`[abs(lab$`PND8 vs PND15`$logFC) >= 1 & lab$`PND8 vs PND15`$adj.P.Val <= 0.05, ]
lab.fc.pnd1 <- lab.fc.pnd$logFC
names(lab.fc.pnd1) <- lab.fc.pnd$Genes

lit.fc.pnd <- lit$`PND7 vs PND14`[abs(lit$`PND7 vs PND14`$logFC) >= 1 & lit$`PND7 vs PND14`$adj.P.Val <= 0.05, ]
lit.fc.pnd1 <- lit.fc.pnd$logFC
names(lit.fc.pnd1) <- lit.fc.pnd$Genes

genes <- intersect(names(lab.fc.pnd1), names(lit.fc.pnd1))

fit <- lm(lit.fc.pnd1[genes] ~ lab.fc.pnd1[genes])

plot_ly() %>%
  add_trace(x = lab.fc.pnd1[genes], y = lit.fc.pnd1[genes], mode = "markers") %>%
  add_trace(x = lab.fc.pnd1[genes], y = predict(fit), mode = "lines") %>%
  layout(
    xaxis = list(title = "PND8 vs PND15 (Lab)"),
    yaxis = list(title = "PND7 vs PND14 (Literature)"),
    title = "SC controls logFC: Lab vs Literature"
  )

PND14/15 vs Adult/PNW8

lab.fc <- lab$`PND15 vs Adult`[abs(lab$`PND15 vs Adult`$logFC) >= 1 & lab$`PND15 vs Adult`$adj.P.Val <= 0.05, ]
lab.fc1 <- lab.fc$logFC
names(lab.fc1) <- lab.fc$Genes

lit.fc <- lit$`PND14 vs Adult`[abs(lit$`PND14 vs Adult`$logFC) >= 1 & lit$`PND14 vs Adult`$adj.P.Val <= 0.05, ]
lit.fc1 <- lit.fc$logFC
names(lit.fc1) <- lit.fc$Genes

genes <- intersect(names(lab.fc1), names(lit.fc1))

fit <- lm(lit.fc1[genes] ~ lab.fc1[genes])

plot_ly() %>%
  add_trace(x = lab.fc1[genes], y = lit.fc1[genes], mode = "markers") %>%
  add_trace(x = lab.fc1[genes], y = predict(fit), mode = "lines") %>%
  layout(
    xaxis = list(title = "PND15 vs Adult (Lab)"),
    yaxis = list(title = "PND14 vs PNW8 (Literature)"),
    title = "SC controls logFC: Lab vs Literature"
  )

SessionInfo

devtools::session_info()
## ─ Session info ───────────────────────────────────────────────────────────────
##  setting  value                       
##  version  R version 3.6.1 (2019-07-05)
##  os       Ubuntu 16.04.6 LTS          
##  system   x86_64, linux-gnu           
##  ui       X11                         
##  language (EN)                        
##  collate  en_US.UTF-8                 
##  ctype    en_US.UTF-8                 
##  tz       Europe/Zurich               
##  date     2019-12-11                  
## 
## ─ Packages ───────────────────────────────────────────────────────────────────
##  package     * version    date       lib source                        
##  assertthat    0.2.1      2019-03-21 [1] CRAN (R 3.6.1)                
##  backports     1.1.5      2019-10-02 [1] CRAN (R 3.6.1)                
##  bookdown      0.16       2019-11-22 [1] CRAN (R 3.6.1)                
##  callr         3.3.2      2019-09-22 [1] CRAN (R 3.6.1)                
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## 
## [1] /home/ubuntu/R/x86_64-pc-linux-gnu-library/3.6
## [2] /usr/local/lib/R/site-library
## [3] /usr/lib/R/site-library
## [4] /usr/lib/R/library
## [5] /home/ubuntu/softwares/anaconda3/pkgs

Deepak Tanwar

Created on: 2019-12-11
Updated on: 2019-12-11